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Added method mergeGVCFs that takes a list of input files. Existing me… #48

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Merged
merged 2 commits into from
May 5, 2025
Merged

Added method mergeGVCFs that takes a list of input files. Existing me… #48

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6478639
Added method mergeGVCFs that takes a list of input files. Existing me…
tcasstevens May 5, 2025
29a3045
Changed bedfile to bedFile in MergeGVCFUtils
tcasstevens May 5, 2025
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12 changes: 7 additions & 5 deletions src/main/kotlin/biokotlin/util/MergeGVCFUtils.kt
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Original file line number Diff line number Diff line change
Expand Up @@ -25,11 +25,13 @@ private val myLogger = LogManager.getLogger("biokotlin.util.MergeGVCFUtils")
*/
object MergeGVCFUtils {

fun mergeGVCFs(inputDir: String, outputFile: String, bedfile: String? = null) {
fun mergeGVCFs(inputDir: String, outputFile: String, bedFile: String? = null) {
mergeGVCFs(getGVCFFiles(inputDir), outputFile, bedFile)
}

runBlocking {
fun mergeGVCFs(inputFiles: List<String>, outputFile: String, bedFile: String? = null) {

val inputFiles = getGVCFFiles(inputDir)
runBlocking {
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Copilot AI May 5, 2025

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Using runBlocking within the mergeGVCFs function may block the calling thread; consider making the function suspend to enable non-blocking asynchronous operations if applicable.

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require(validateVCFs(inputFiles).valid) { "Some GVCF files are invalid." }

Expand Down Expand Up @@ -70,12 +72,12 @@ object MergeGVCFUtils {

}

val theBedfile = bedfile?.trim()
val theBedfile = bedFile?.trim()
if (theBedfile.isNullOrEmpty()) {
myLogger.info("Writing output: $outputFile")
writeOutputVCF(outputFile, samples, variantContextChannel)
} else {
myLogger.info("Writing output files with base name: $outputFile and bedfile: $bedfile")
myLogger.info("Writing output files with base name: $outputFile and bedfile: $bedFile")
writeOutputVCF(outputFile, theBedfile, samples, variantContextChannel)
}

Expand Down